January 23, 2013

Genetic evidence for the colonization of Australia

Quaternary International
Volume 285, 8 February 2013, Pages 44–56

Genetic evidence for the colonization of Australia

Sheila van Holst Pellekaan et al.

Mitochondrial DNA (mtDNA), Y-chromosome and, more recently, genome studies from living people have produced powerful evidence for the dispersal of modern human populations. The prevailing model of global dispersion assumes an African origin in which Australia and the American continents represent some of the extreme regions of human migration, though the relative timing of dispersal events remains debatable. Here, a focus on Australia and New Guinea discusses currently available genetic evidence from the two regions, compared with that from Asia. Mt haplotypes indicate ancient ancestry for both Australia and New Guinea peoples, with evidence of some shared genetic connection and other unshared haplogroups apparently specific to both places. Migration into Sahul from south-east Asia may have been by more complex routes than only along a ‘southern coastal route’, raising the question of possible common ancestry in central or northern Asia for some Australian and American peoples for which current genetic evidence is tenuous. Although current dating methods for genetic diversity rely heavily on several assumptions, best estimates provide support for archaeological dates, indicating that, relative to the colonization of America, Australia was inhabited very early. Genetic diversity of living descendants of Australia’s founding populations is informative for dispersal within Australia and for understanding complex population histories of Asia.

30 comments:

"Mt haplotypes indicate ancient ancestry for both Australia and New Guinea peoples, with evidence of some shared genetic connection and other unshared haplogroups apparently specific to both places."

See this comment by Gregory76. Part of it is jumbled and should instead read

"this suggests that male K Murrayans killed off the Negrito males (presumably D or a descendant) and married their widows, and later M evolved from K in their descendants, or that M had already evolved from K and male M Murrayans killed off the Negrito males and married the widows."

"Migration into Sahul from south-east Asia may have been by more complex routes than only along a ‘southern coastal route’, raising the question of possible common ancestry in central or northern Asia for some Australian and American peoples for which current genetic evidence is tenuous."

Ainoids. The Murrayians of Birdsell's Australian trihybrid theory. In 1951 Birdsell published "The Problem of the Early Peopling of the Americas As Viewed from Asia", in which he wrote:

"The reconstructed patterning of peoples in Eastern Asia, as well as the scanty archaeological evidence, suggests a dihybrid origin for the American Indians. The two racial elements present at the proper time and place for the peopling of the New World were Amurians and Mongoloids."

The biggest remaining open issue in the peopling of Sahul, which we actually understand quite well compared to most of the world, because there are fewer layers in the palmpiset, is the extent to which the linguistic diversity of Northern Australian aboriginal languages reflects one or more subsequent prehistory migrations or trade-bride exchange relationships in the Holocene.

A paper a few weeks ago suggests that there was at least one such wave of Ancestral South Indian-like populations around the time that the Dingo was introduced.

This paper seems to be looking instead more at the ethnogenesis of the initial wave of migration to Sahul, in the context of the larger modern human dispersal Out of Africa, but the abstract is pretty stingy about the conclusions reached. The money statements (themselves full of hedges noted by emphasis below) are that:

"Migration into Sahul from south-east Asia may have been by more complex routes than only along a ‘southern coastal route’, raising the question of possible common ancestry in central or northern Asia for some Australian and American peoples for which current genetic evidence is tenuous. . . . Genetic diversity of living descendants of Australia’s founding populations is informative . . . for understanding complex population histories of Asia."

A partial Central or North Asian origin for American peoples is utterly unimpressive. A partial Central or North Asian origin for Australian peoples, in contrast, would be a major paradigm shift - since it would implicate Northern route migration ca. 50,000 kya (allowing a few thousand years to migrate from Eastern Europe or Northern India, to Siberia, to Australia) for which there is no archaelogical or megafauna extinction evidence of which I am aware.

The earliest evidence of modern humans in North and Central Asia to the best of my recollection (based on archaeology and evidence of megafauna extinctions) date to more like 30,000 kya, far too late to influence the composition of the founding populations of Sahul. This is one reason that others have seen genetic links between Southern route Asia and Northern route Asia as mostly from South to North.

"Migration into Sahul from south-east Asia may have been by more complex routes than only along a ‘southern coastal route’, raising the question of possible common ancestry in central or northern Asia for some Australian and American peoples for which current genetic evidence is tenuous".

That is what I have been suggesting for years. As to 'current genetic evidence is tenuous', I would mention Y-DNA C and mt-DNA N for both of which it is extremely difficult to imagine a southern route.

"Genetic diversity of living descendants of Australia’s founding populations is informative for dispersal within Australia and for understanding complex population histories of Asia".

Someone insisted that Y-DNAs C and K were evenly distribtuted through Australia. I doubt such to be the case but does anyone have any data on the two haplogroups' distribution in Australia?

"this suggests that male K Murrayans killed off the Negrito males (presumably D or a descendant) and married their widows"

Until Y-DNA D is found at least somewhere close to Australia or New Guinea that hypothesis can only be very doubtful.

5-4 ka - Y C and mt N Veddoids, driven from India by the Caucasoids of the Indus Valley Civilization, expand down the Malay Peninsula, across the Sunda Islands, and finally from Timor to the adjacent coast of Australia.

A partial Central or North Asian origin for Australian peoples, in contrast, would be a major paradigm shift

For those unfamiliar with ideas that had permeated even into Australian children's books of the 50s and early 60s, and who are informed only by post-60s PC anthropology, yes, it must come as quite a shocker.

since it would implicate Northern route migration

There never was any "Northern route".

ca. 50,000 kya

Murrayians came in between 40 and 35 ka.

(allowing a few thousand years to migrate from Eastern Europe or Northern India, to Siberia, to Australia) for which there is no archaelogical or megafauna extinction evidence of which I am aware.

Because it didn't happen.

This is one reason that others have seen genetic links between Southern route Asia and Northern route Asia as mostly from South to North.

The earliest evidence of modern humans in North and Central Asia to the best of my recollection (based on archaeology and evidence of megafauna extinctions) date to more like 30,000 kya

Andrew,

No - the general assumption is ~45,000 to 40,000 ya for Central Asia and southern Siberia. Note that the Tianyuan specimen is 40,000ya. And anything older than that is much more difficult to date.

I have no doubt that people reached central and northern Asia by more than a single, coastal route. And since they lived there for such a long time, small groups of them were able to migrate many places even before LGM, including Europe (admixture must have happened before or during early Gravettian).

Or look at mtDNA B - which is found in Nicobar, Polynesia, and the Americas - but apparently was first present in Central-Eastern Asia ~40,000-45,000ya.

Someone insisted that Y-DNAs C and K were evenly distribtuted through Australia. I doubt such to be the case but does anyone have any data on the two haplogroups' distribution in Australia?

I never said that they were "evenly distributed through Australia". What I said was

"As far as I can tell, K and C are both widespread throughout Australia, which would mean that 4000 years was sufficient for the thorough interdiffusion of the Murrayian and Carpentarian elements."

To which you responded

Any reference for that? The only information I have is what Ebizur provided at Maju's blog some time back. He only differentiated between Arnhem and the desert but K-M9 made up 30% in Arnhem but only 17% in the desert. It would surely be surprising if both haplogroups are evenly distributed through a continent. The only case ever I would think.

Those numbers come from this paper. They were the same numbers that I was familiar with, and seeing that the C and K frequencies were similar in two different parts of Australia, I assumed that they were probably similar throughout Australia. Now that I've had time to dig in to several papers, I know that that was a foolish assumption. There are very few data available, but let's drill down into what we have.

In the above paper, the first set of samples was from Arnhem Land. There C was 63.3% and K was 30.0%. The second set of samples was from Balgo in the Great Sandy Desert, and Christmas Creek, Derby, Looma, and Turkey Creek elsewhere in Kimberley. For that set C was 68.7% and K was 17.1%. Now Kimberley is exactly where the Veddoids coming from Timor would have made landfall, and it is where non-Pama-Nyungan languages are spoken. Arnhem Land is farther away from where the Veddoids came ashore, and in northeast Arnhem Land there is an exclave of Pama-Nyungan (Yolngu), while in much of the rest of Arnhem Land there are languages which are in some places classified as non-Pama-Nyungan, but in other places as Macro-Pama-Nyungan (Arnhem or Macro-Gunwinyguan languages). So if the Veddoids were C and the Ainoids were K, then we would expect C to be more frequent in Kimberley than in Arnhem Land, and K to be more frequent in Arnhem Land than in Kimberley. And, indeed, that is exactly what we see.

Here is a second paper. They had samples from Kalumburu, which is in Kimberley. Now all of the places in Kimberley except for Derby from which samples were obtained in the first paper are a great distance inland. Kalumburu, like Derby, is a coastal town, but Kalumburu is at about the exact spot on the coast of Australia that has the minimal distance to Timor, while Derby is further south. And what haplogroup frequencies did they find in Kalumburu? 100% C.

Here is a third paper, and here is its supplementary material. The paper never says exactly where they got their Australian samples from, but it does have a map which shows that they came from somewhere in the region in which Garawan languages are spoken. The Garawan languages are like the Arnhem languages in that they are sometimes classified as non-Pama-Nyungan and other times as Macro-Pama-Nyungan, but the Garawan languages, along with the Tangkic languages and Pama-Nyungan proper, are thought to belong to a subfamily within Macro-Pama-Nyungan, called Greater Pama-Nyungan. In fact, between Tangkic and Garawan, the Garawan languages are thought to be the ones more closely related to Pama-Nyungan proper. Now, based on the postulated relationship between Veddoids, Hg C, and non-Pama-Nyungan languages, and between Ainoids, Hg K, and Pama-Nyungan languages, we would expect an elevated frequency of K in this sample. The sample's frequencies were 48.5% C, 42.4% K. Theory confirmed.

So, in summation, I would expect that with a large set of data covering the whole of Australia, we would see a decreasing frequency of C with increasing distance from Timor, and a decreasing frequency of K with increasing distance from the Murray River.

Genetiker,I agree that the migrants to the Americas can be divided into a more Mongoloid group and a less Mongoloid group, as Coon and: the former is more brachycephalic and stronger in the eastern parts of the two continents, and more often practiced agriculture.I would go further and subdivide these two groups, as others have done. They may have originally corresponded to the 4 main female haplotypes. I suggest the following:D (original male partner D) from Andamanoids: early South American dolichocephals (Imbelloni’s Fuegids and Laguids), speaking Ge-Pano-Carib: C (original male partner C) from Veddoids: North American dolichocephals (Imbelloni’s Planids), speaking Algonkian-Wakashan, and maybe later South American dolichocephals (Imbelloni’s Amazonids), speaking EquatorialB (original male partner 0) from central Mongoloids: various brachycephals (Imbelloni’s Pueblo-Andids and Isthmids), speaking Aztec-Tanoan, Macro-Oto-Manguean, Macro-Chibchan and AndeanA (original female partner to Q, which killed the other males) from Eskimos: various brachycephals: Penutian-speakers (associated with Imbelloni’s Columbids), Nadene-speakers (not associated with a separate group by Imbelloni) and Eskimos.

Terry, In reply to my statement:"later M evolved from K in their descendants, or that M had already evolved from K and male M Murrayans killed off the Negrito males and married the widows". you said:"Another problem. No Y-DNA M in Australia. M is a New Guinea/Melanesian haplogroup."

I reply: in this part of my discussion I was only talking about New Guinea.

I'm going to need a lot more time to think about your comment on the Americas, but I want to say now, before the post gets any further down the page, that the more I think about it, the less crazy it seems, and the more brilliant it seems.

There is very little of either Y-DNA C* or mt-DNA N* anywhere in India.

"Kalumburu is at about the exact spot on the coast of Australia that has the minimal distance to Timor, while Derby is further south. And what haplogroup frequencies did they find in Kalumburu? 100% C".

To me it appears almost certain that the first Australians arrived from Timor, so that would mean that this finding supports the idea that those first people were Y-DNA C. It doesn't fit your idea of a different entry point for your postulated second entry.

"Now Kimberley is exactly where the Veddoids coming from Timor would have made landfall"

I agree it is exactly where any arrivals from Timor would land, Veddoids or otherwise.

"Arnhem Land is farther away from where the Veddoids came ashore"

And note:

"from Arnhem Land. There C was 63.3% and K was 30.0%. The second set of samples was from Balgo in the Great Sandy Desert, and Christmas Creek, Derby, Looma, and Turkey Creek elsewhere in Kimberley. For that set C was 68.7% and K was 17.1%".

So there is a higher proportion of K in Arnhem land, which fits K having arrived there rather than in the Kimberleys. languages perhaps cannot tell us too much as they are adopted or discarded for a variety of reasons, but non-Pama-Nyungan languages are basically confined to northwest Australia and so are possibly the later arrivals in that region.

"Ainoids, Hg K"

If that connection is in fact correct it would indicate the people are not very well named. Ainu are mostly y-DNA C1 and D. K is present only in the very derived form of O and that is probably a product of Neolithic arrival.

"we would expect an elevated frequency of K in this sample. The sample's frequencies were 48.5% C, 42.4% K. Theory confirmed".

Which theory? That K is probably a later arrival because it is found at higher frequencies in northern Australia?

"in this part of my discussion I was only talking about New Guinea".

Apologies. Unfortunately I just took what Genetiker wrote and didn't go back to your original comment.

"A (original female partner to Q, which killed the other males)"

That's a fairly extreme view. I have my reseravtions about accepting that idea.

One problem that I see is that there appears to be a clear relationship between Y C and Na-Dene languages. Everywhere Na-Dene is found, C is found, and everywhere that C is not found, Na-Dene is also not found.

There is very little of either Y-DNA C* or mt-DNA N* anywhere in India.

Compared to where?

To me it appears almost certain that the first Australians arrived from Timor, so that would mean that this finding supports the idea that those first people were Y-DNA C.

Are the aboriginals in the areas in which C is most frequent more Veddoid or more Ainoid?

According to the recent autosomal analysis, when did the Veddoids arrive?

It doesn't fit your idea of a different entry point for your postulated second entry.

Where did I say the second entry occurred?

If that connection is in fact correct it would indicate the people are not very well named. Ainu are mostly y-DNA C1 and D. K is present only in the very derived form of O and that is probably a product of Neolithic arrival.

If members of a race in one area have one set of Hgs, do all members of that race in all other areas have that same set of Hgs?

Which theory? That K is probably a later arrival because it is found at higher frequencies in northern Australia?

Is K more frequent in areas in which non-Pama-Nyungan languages are spoken, or in areas in which Macro-Pama-Nyungan languages are spoken?

The fact that the Paleo-Indian waves were Ainoid suggests that they probably arrived in the Americas not long after 40 ka, and in quick succession. (This would explain Monte Verde I.) The present distribution of D and B shows that they took a Pacific coastal route.

The fact that the Neo-Indian waves were Mongoloid means that they arrived after 25 ka. The present distribution of C and A shows that they took a Bering Straight route.

Genetiker,So you have switched B and C around from my model, as regard degrees of Mongoloidness and head length. What is your reason for doing so? B still seems to found mainly in the area from the southwestern U.S. through the Andes, which is mostly brachycephalic and at least as Mongoloid as the eastern sides of the continents. (More precisely, while western North America seems most Mongoloid and eastern South America least Mongoloid, western South America and eastern North America seem intermediate, typically Amerind in their phenotype). More promising is your shifting of C to the brachycephalic side, as it is strong in the southwestern U.S., and in the Amazon, where the later arrivals were probably more brachycephalic than the earlier ones.

As to the Nadene, I would be very pleased to separate them from the others in the A-group, since they and the Penutians and the Eskimos are heterogeneous phenotypically and linguistically. But though the Nadene seem distinctive in their male haplotype, being mostly C, they don’t seem to be so in the female haplotypes, but perhaps I am wrong.

So you have switched B and C around from my model, as regard degrees of Mongoloidness and head length. What is your reason for doing so?

My reasoning was purely inferential. First, the ages of B and D (50 ka and 38 ka) indicate to me that they were involved in Ainoid evolution, while the ages of C and A (both 24 ka) indicate to me that they were involved in Mongoloid evolution. Tianyuan was B, and I believe that Tianyuan was Ainoid. Second, of the four American mt Hgs, B is the only one that is not found (except perhaps at very low frequencies) in North Asia. Instead it is most frequent in East Asia. I believe that Ainoid evolution occurred in East Asia, and Mongoloid evolution occurred in North Asia. Third, B and D are found in the Ainu, but not C. Fourth, the distribution of B indicates to me that it arrived by a Pacific coastal route. I believe that the Ainoids came in early by Pacific coastal routes and that the Mongoloids came in later by Bering Strait routes. Fifth, Dienekes' f3-statistics on craniometric data show that North and South Japanese skulls are mixtures of Eskimo skulls and Peruvian skulls. I believe that the Eskimo relationship is due to the Mongoloid Yayoi element in the Japanese, and that the Peruvian relationship is due to the Ainoid Jomon element in the Japanese and a significant Ainoid, mt B, Paleo-Indian element in Peruvians.

Here is a revision of my timeline, which accounts for the times when the different routes were available:

22 ka - mt B4b Ainoids migrate from East Asia to the Americas by a Pacific coastal route

19 ka - mt D4 Ainoids migrate from East Asia to North Asia, and then to the Americas by a Pacific coastal route

16 ka - mt C1 Mongoloids migrate from North Asia to the Americas by a Bering Strait route

14 ka - mt A2 Mongoloids migrate from North Asia to the Americas by a Bering Strait route

"Are the aboriginals in the areas in which C is most frequent more Veddoid or more Ainoid?"

Sorry, I'm not sure what your distinction between the two is.

"Is K more frequent in areas in which non-Pama-Nyungan languages are spoken, or in areas in which Macro-Pama-Nyungan languages are spoken?"

I don't know. That's why I was interested in any information you had.

"Which languages 'are possibly the later arrivals in that region'?"

Non-Pama-Nyungan is confined to the northwest of Australia. The remaining languages are Pama-Nyungun. On Pama-Nyungan:

http://en.wikipedia.org/wiki/Pama%E2%80%93Nyungan_languages

Non-Pama-Nyungan:

http://en.wikipedia.org/wiki/Non-Pama%E2%80%93Nyungan_languages

Quote:

"It is often noted that it is odd for one family to dominate so much of a continent when the speakers are not agricultural and have no technological advantage over their neighbors. Johanna Nichols suggests that the northern families may be relatively recent arrivals from the Malay archipelago, perhaps later replaced there by the spread of Austronesian. That could explain the typological difference between Pama–Nyungan and non-Pama–Nyungan languages, but not how a single family came to become so widespread".

"First came the Negritos. These were then swept aside by the Murrayians, a heavily built brown-skinned wavy-haired people, who pushed the Negritos to Far North Queensland, but in Tasmania intermixed with them. Finally came the slender, black, also wavy-haired Carpentarians, who restricted the Murrayians to the Southeast of the continent, and populated most of the tropical north."

"There were three major waves of migration of quite different ancient people who came to the Australian continent from southeast Asia. More than 40,000 years ago, when sea levels were much lower and Australia, New Guinea and Tasmania comprised one landmass, called Sahul, the first to arrive were a slightly-built people of pygmoid stature with dark skin and very frizzy hair. They were Negritos (named after the Spanish "little negro"), and they provided the initial population for the whole of this Greater Australia. About 20,000 years ago, a second type of people arrived from Asia. These newcomers, called Murrayians, were comparatively lightly skinned, wavy-haired, stocky in build, with a lot of body hair. They drove the Negritos before them until the latter retreated to the highlands of New Guinea, the rainforests of North Queensland and to then ice-capped Tasmania. The Murrayians became the dominant population on the east coast of Australia, and the open grasslands and parklands of the south and west of the continent. Then, about 15,000 years ago, a third wave of hunter-gatherers arrived. They were comparatively tall, straight-haired and dark skinned, with very little body hair. Named Carpentarians, they colonised northern and central Australia."

Genetiker,Your reasoning is plausible, and I could accept shifting of C to the brachycephalic side. But B still seems to found mainly in the area from the southwestern U.S. through the Andes, which is mostly brachycephalic and more Mongoloid than the eastern sides of the continents. You say:

the ages of B and D (50 ka and 38 ka) indicate to me that they were involved in Ainoid evolution, while the ages of C and A (both 24 ka) indicate to me that they were involved in Mongoloid evolution.

I would say that the degree of Mongoloidness and brachycephaly depend on how much time was spent in a very cold environment rather than age of arrival.

You say:Tianyuan was B, and I believe that Tianyuan was Ainoid.

Perhaps its ancestors had not passed through a cold enough environment long enough before.

You continue:Second, of the four American mt Hgs, B is the only one that is not found (except perhaps at very low frequencies) in North Asia. Instead it is most frequent in East Asia. I believe that Ainoid evolution occurred in East Asia, and Mongoloid evolution occurred in North Asia.

I think C and D moved in the most easterly areas through both regions, while A and B came from the west with A taken a northern route to North Asia and B a southern route to East Asia.

Third, B and D are found in the Ainu, but not C.

B being common in East Asia and D being common along the coast.

Fourth, the distribution of B indicates to me that it arrived by a Pacific coastal route.

B seems to be widespread on the western (Pacific) side of the continents from the U.S. southwest south to the Andes, so I would think it could come by either a coastal or an interior route.

I believe that the Ainoids came in early by Pacific coastal routes and that the Mongoloids came in later by Bering Strait routes. Fifth, Dienekes' f3-statistics on craniometric data show that North and South Japanese skulls are mixtures of Eskimo skulls and Peruvian skulls. I believe that the Eskimo relationship is due to the Mongoloid Yayoi element in the Japanese, and that the Peruvian relationship is due to the Ainoid Jomon element in the Japanese and a significant Ainoid, mt B, Paleo-Indian element in Peruvians.

I am inclined to think that the Mongoloid Yayoi element was associated with B (the Yayoi B being descended, via the Koreans, from Tungus of the Baikal type, which spent much time in Siberia and so became cold-adapted, but the B that passed to the Americas did not stay in the north as long).

"What is the frequency of C* in India? What is the frequency of C* in Southeast Asia?"

Maju and I were arguing that point at his blog, but it takes so long to download that blog. It seems almost all C in India is C5 with C* being very much a minority in what is a minority presence of C anyway. C* has bee recorded through island SE Asia as far south as the Lesser Sunda Islands where it tends to be replaced by C2.

"Birdsell's trihybrid theory"

Seems to be out of favour at the moment. That is not say it is incorrect of course.

"Now do you understand it?"

Seems to me that the Ainu are the most different from the other three. Some Ainu are in New Zealand at present as guests of the local Maori. Most of them look like ordinary Japanese but that is presumably because of interbreeding.

"The answer was B, Macro-Pama-Nyungan".

Y-DNA B is African and mt-DNA B is almost unknown in Australia. And in Melanesia it is almost certainly associated with the Austronesian expansion, not ealrier.

C is the only Y-DNA connection between Australia (C4-M347) and Japan (C1-M8). In one direction or the other. We need a better resolution of Y-DNA C to tell which one.

To me Australia is the clue to everything. We have a reasonably good idea of processes occurring north and east of Australia, especially those happening during the last three thousands years as people moved from SE Asia out into the Pacific. From that we can follow the threads back and construct a fairly good scenario as to what had been happening in SE Asia immediately prior to that. I'm confident we can even follow the threads further back. But we still don't know what was happening in Australia, where humans arrived at least 46,000 years ago. Once we sort that out we will be better able to sort out what had been happening in Eurasia before humans arrived in Australia.

The only information I have concerning Australian Y-DNA is from what Ebizur posted at Maju's old blog. There he showed that of 60 Aboriginals from Arnhem Land and 35 from the Desert:

C4a: Arnhem Land: 53.5%Australian Desert: 68.6%

But, very interestingly, he shows what to me is most likely

C4(xC4a): Arnhem Land: 10% Australian Desert: nil

The other main haplogroup listed is to me most likely

K-M9(xK2,K3,M,NO,P,S), but could be what is now K1-P60: Arnhem Land: 30% Australian Desert: 17.1%

That presumably means no more than that both Y-DNA C and Y-DNA K arrived in northern Australia and spread from there. But did both arrive at the same time? To me it looks as though K is a later immigrant, or a follower.

"At least 1,000 Aboriginal founders first arrived in Australia some 50,000 years ago, a reconstruction indicates — numbers that could be evidence of an intentional migration rather than the accidental stranding of a few individuals at a time. The study also finds that the population was devastated during the latest Ice Age, but later rebounded".

The ice age bit solves the problem regarding the widespread single language family.

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